Chapter 10- Biochemistry of the genome Flashcards
Friedrich Miescher
The first person to isolate phosphorus-rich chemicals from leukocytes from pus samples. These chemicals would later be known as DNA and RNA, but he named the chemicals “nuclein”. They were later called nucleic acid
Albrecht Kossel
Isolated and characterized the 5 different nucleotides bases composing nucleic acid (adenine, guanine, cytosine, thymine in DNA, and uracil in RNA).
Gregor Mendel
Demonstrated the basic patterns of inheritance using pea plants. Mendel performed hybridizations, which involve mating two true-breeding individuals (P generation) that have different traits, and examined the characteristics of their offspring (first filial generation, F1) as well as the offspring of self fertilization of the F1 generation (second filial generation, F2). He found that traits are transmitted from parents to offspring independently of other traits
Chromosomal Theory of Inheritance
Identifies chromosomes as the genetic material responsible for Mendelian inheritance. The theory was developed even before there was evidence that traits were carried in chromosomes
Thomas Hunt Morgan
Carried out crosses with fruit flies. They observed fly chromosomes microscopically and correlated the observations with the resulting fly characteristics. Their
work provided the first experimental evidence to support the Chromosomal Theory of Inheritance in the early 1900s
Barbara McClintock
Developed chromosomal staining techniques to visualize and differentiate between the different chromosomes of corn. She also found that certain loci could change position within the chromosome. These jumping genes are now called transposons and are mobile segments of DNA that can move within the genome of an organism. They regulate gene expression, protein expression, and virulence
Why are microbes and viruses good models for studying genetics?
They are propagated more easily in the laboratory and grow to high population densities in a short period of time. They can also be genetically manipulated. All organisms have the same underlying molecules responsible for heredity, so microbes can be studied regardless of their many differences between other organisms
Hammerling experiments
He studied large algal cells (Acetabacteria). These cells grow a “foot” that contain a nucleus and are used for substrate attachment. Hammerling removed either the cap or the foot of the cells and observed whether new caps or feet were regenerated. Only the cap could regenerate, which suggests that the hereditary information is found in the foot of each cell, which contains the nucleus. He also grafted head or tail portions of one cell onto another cell. The caps of the cells developed their morphology to the nucleus of each grafted cell
Red bread mold model (Beadle and Tatum)
Researchers irradiated the mold with X-rays to induce changes (mutations) to a sequence of nucleic acids. They mated the irradiated mold spores and attempted to grow them on both a complete medium and a minimal medium. Molds that grew on a complete medium but not not grow in the minimal medium lacking vitamins and amino acids theoretically contained mutations in the genes that encoded biosynthetic pathways. They were able to find these mutations and therefore demonstrated the relationship between genes and the proteins they encode
One gene-one enzyme hypothesis
Suggests that each gene encodes one enzyme. Demonstrated through work by Beadle, Tatum, and colleagues. They discovered mutations in the arginine biosynthesis pathway and supplemented these mutations with intermediates (citrulline or ornithine) in the pathway. The three mutants differed in their abilities to grow in each of the media
Griffith’s transformation experiments
Griffith was the first person to show that heredity information could be transferred from one cell to another between members of the same generation (horizontally) rather than vertically, between parents and offspring. He used a rough, nonpathogenic R strain of streptococcus bacteria and a pathogenic S strain. When mice were injected with the live S strain, they died. The mice survived when injected with the live R strain or the heat-killed S strain. But when he injected the mice with a mixture of live R strain and heat-killed S strain, the mice died. Upon isolating the live bacteria
from the dead mouse, he only recovered the S strain of bacteria. When he then injected this isolated S strain into fresh mice, the mice died. Griffith concluded that something had passed from the heat-killed S strain into the live R strain and “transformed” it into the pathogenic S strain; he called this the “transforming principle.”
Avery, MacLeod, and McCarty’s research (1944)
They further explored Griffith’s transforming principle. They isolated the S strain from infected dead mice, killed it using heat, and inactivated various components of the S extract. They used degrading enzymes that could destroy proteins, RNA, and DNA. They found that when DNA was degraded, the resulting extract was no longer able to transform the R strain. No other enzymatic treatment was able to prevent transformation, leading to the conclusion that DNA was the transforming principle and that genetic information could be transferred horizontally
Hersey and Chase
Provided evidence that DNA was the genetic material rather than protein. They studied a T2 bacteriophage virus that infected E. coli bacteria. They labeled the protein coat in one batch of phage using radioactive sulfur, because sulfur is found in the amino acids methionine and cysteine but not in nucleic acids. They labelled the DNA in another batch using radioactive phosphorus because phosphorus is found in DNA and RNA. The samples were centrifuged and placed in tubes- lighter phage particles remained in the supernatant and heavier bacterial cells remained at the bottom of the tube. In the protein tube, the radioactivity remained only in the supernatant. In the DNA tube, the radioactivity was detected only in bacterial cells. They concluded that it was the phage DNA that was injected into the cell that carried the information to make more phage particles, so DNA was the source of genetic material
Nucleic acids
Biological macromolecules that have monomers called nucleotides.
Base sequence
The order that nucleotides appear within a strand. The base sequence of DNA carries the hereditary information in a cell
Deoxyribonucleotides
Nucleotides that compose DNA
Nucleoside
Composed of the 5 carbon sugar and nitrogenous base
3 components of a deoxyribonucleotide
- Deoxyribose- a 5 carbon sugar
- A phosphate group
- A nitrogenous base- a ring structure that is responsible for complementary base pairing between nucleic acid strands
Purines
Bases that have a double ring structure with a 6 carbon ring fused to a 5 carbon ring. They include adenine and guanine
Pyrimidines
Bases that are smaller, and contain only a 6 carbon ring structure. Includes cytosine and thymine
Phosphodiester bonds
Covalent bonds that connect the nucleotides of the DNA molecule. The phosphate group attached to the 5’ carbon of the sugar of one nucleotide is bonded to the hydroxyl group of 3’ sugar of the other nucleotide
Sugar-phosphate backbone
The alternating sugar-phosphate structure that makes up the framework of a nucleic acid strand. It is held together by phosphodiester bonds
Chargaff’s rules
The idea that in DNA, the amount of adenine to close to equaling the amount of thymine, and the amount of cytosine is close to equaling the amount of guanine
Rosalind Franklin
Produced well-defined X ray images of DNA that clearly showed its double helix structure
Watson and Crick
Discovered the purine-pyrimidine pairing of the double helical DNA molecule. They proposed that the strands twist around each other to form a right handed helix and that the two strands are antiparallel
Antiparallel
The 3’ end of one DNA strand faces the 5’ end of the other strand
3’ end
Contains a free hydroxyl group
5’ end
Contains a free phosphate group
DNA structure
The sugar and phosphate of the nucleotides form the backbone of the structure, while the nitrogenous bases are stacked inside and form base pairs. There are approximately 10 bases per turn in DNA. The sugar-phosphate backbones are spaced asymmetrically, which creates major grooves and minor grooves (where the backbone is close together). These grooves are where proteins can bind to DNA and change its structure or regulate replication or transcription
Complementary base pairs
Base pairs are formed between a purine and a pyrimidine. A pairs to T and C pairs to G
The base pairs are stabilized by
Hydrogen bonds. A and T form 2 hydrogen bonds between them, and C and G form 3 hydrogen bonds between them
DNA denaturation
When the hydrogen bonds between 2 complementary bases are broken and the DNA separates into 2 single strands. This occurs due to high temperatures or certain chemicals. The hydrogen bonds can reform if the molecule is cooled or if the chemical denaturants are removed
Vertical gene transfer
The transmission of genetic information from mother to daughter cells. It occurs through DNA replication when a cell divides and distributes the DNA into the new daughter cells.
Ribonucleotides
Make up RNA and are linked by phosphodiester bonds
3 components of ribonucleotides
- Ribose- a 5 carbon sugar
- Nitrogenous base (A, U, G, and C)
- A phosphate group
Why is DNA used for storing genetic information?
There are structural differences between ribose and deoxyribose, which makes DNA more stable. RNA is relatively more unstable, which makes it more useful for short term functions
Uracil
A pyrimidine that base pairs with adenine, only found in RNA
RNA structure
Single stranded. There is intramolecular base pairing between complementary sequences within the RNA strand. This creates a 3D structure that is essential for their function
General function of RNA
Cells access the information stored in DNA by creating RNA to direct the synthesis of proteins. Proteins are synthesized through translation
3 types of RNA involved in protein synthesis
- Messenger RNA (mRNA)
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
Messenger RNA (mRNA)
The intermediary between DNA and its protein products. mRNA is like a “photocopy” of specific information that is needed to make a necessary protein. If a cell requires a protein, the gene for this product is “turned on” and the mRNA is synthesized through transcription. The mRNA then interacts with the ribosomes to synthesize the protein during translation. mRNA is unstable and short lived so that proteins are only made when necessary
rRNA and tRNA
Stable types of RNA. They are encoded in DNA and then copies into long RNA molecules that are cut to release smaller fragments containing the individual mature RNA molecules. They are synthesized into ribosomes in the nucleolus region in eukaryotic cells. These types of RNA don’t carry instructions to direct the synthesis of a protein, but they play other roles in protein synthesis
rRNA functions
Make up ribosomes, along with proteins. It provides a location for mRNA to bind on the ribosome. rRNA ensures the correct alignment of the mRNA, tRNA, and ribosomes. It also plays a catalytic role in the ribosomes. It catalyzes the formation of the peptide bonds between 2 aligned amino acids during protein synthesis
tRNA functions
tRNA is the smallest type of RNA. It carries the correct amino acid to the site of protein synthesis in the ribosome. Base pairing occurs between tRNA and mRNA, allowing for the correct amino acid to be inserted into the protein chain.
Genome
All of an organism’s genetic material
Genes
Segments of DNA molecules. Individual genes contain the instructions necessary to make proteins, enzymes, or stable RNA molecules
Genotype
The full collection of genes contained in a cell’s genome. The genotype remains constant
Phenotype
The set of genes that are expressed at any point in time. This determines the cell’s activities and its observable characteristics. The cell turns on and off certain genes when necessary. Phenotype can change in response to environmental signals
Constitutive genes
Genes that are always expressed. Some of these genes are “housekeeping” genes because they’re necessary for the basic functions of the cell
Chromosomes
Discrete DNA structures within cells that control cellular activity. Chromosomes are found in the nucleus of eukaryotic cells, and prokaryotic cells have one circular chromosome in the cytoplasm
Diploid
Cells that contain two copies of each chromosome
DNA supercoiling
The process by which DNA is twisted to fit inside the cell. Chromosomes need to be packaged into a small space to fit inside the cell, as the length of a chromosome exceeds the length of the cell
Structure of chromosomes in eukaryotic cells
The chromosomes are linear, and eukaryotic cells contain multiple distinct chromosomes. Many eukaryotic cells are diploid
Topoisomerases
Enzymes involved in supercoiling. They help to maintain the structure of supercoiled chromosomes and prevent the overwinding of DNA during cellular processes, like replication
Histones
DNA binding proteins that perform DNA wrapping and attachment to scaffolding proteins. In eukaryotes, the packaging of DNA by histones may be influenced by environmental factors that affect the presence of methyl groups on certain cytosine nucleotides of DNA.
Chromatin
The combination of DNA with its attached scaffolding proteins
Epigenetics
The influence of environmental factors on DNA packaging. The packaging of DNA by histones can be influenced as environmental factors affect the presence of methyl groups on DNA’s cytosine nucleotides. Epigenetics is a mechanism for regulating gene expression without altering the sequence of nucleotides. Epigenetic changes can be heritable because they can be maintained through multiple rounds of cell division
Haploid
Cells that only have one copy of each gene- this describes prokaryotes
Organization of prokaryotic chromosomes
Chromosomes in bacteria and archaea and circular, and they only have one chromosome. These cells also require supercoiling and use topoisomerases for this process. They have histone-like proteins that help with DNA packaging. Different regions of DNA are packaged differently, so some regions of chromosomal DNA are more accessible to enzymes. These regions are typically used as templates for gene expression
DNA gyrase
A type of topoisomerase found in bacteria and some archaea that helps prevent the overwinding of DNA. It is a target of some antibiotics
Noncoding DNA
Regions of the genome that do not encode proteins or stable RNA products. Noncoding regions are typically found in areas prior to the start of coding sequences of genes and in DNA sequences located between genes. Some noncoding DNA may contribute to the regulation of transcription or translation by helping with DNA packaging, chromosomal stability, and through producing small noncoding RNA molecules
Prokaryotic vs eukaryotic noncoding DNA
In prokaryotes, around 12% of the genome is noncoding. In eukaryotes, around 98% of the genome is noncoding
Extrachromosomal DNA
Additional molecules of DNA outside the chromosomes. This includes DNA from organelles like the mitochondria or chloroplasts. In addition, the genomes of some DNA viruses can be maintained independently in the host cell during a latent infection. Plasmids are an example in prokaryotes
Plasmids
Smaller loops of extrachromosomal DNA found in some prokaryotes. Plasmids contain genes that are not essential for normal growth
Horizontal gene transfer
The process of bacteria exchanging plasmids. It can provide microbes with new genes that are beneficial for growth and survival under special conditions. Plasmids can encode virulence factors that make a microbe pathogenic or give it the ability to resist antibiotics
